// static
CEvaluationNode * CEvaluationNodeDelay::fromAST(const ASTNode * pASTNode, const std::vector< CEvaluationNode * > & children)
{
assert(pASTNode->getNumChildren() == children.size());
size_t i = 0, iMax = children.size();
SubType subType = SubType::DELAY;
std::string data = "delay";
CEvaluationNode * pConvertedNode = new CEvaluationNodeDelay(subType, data);
for (i = 0; i < iMax; ++i)
{
pConvertedNode->addChild(children[i]);
}
pConvertedNode->compile(NULL);
return pConvertedNode;
}
//TODO remove pModel
CEvaluationNode* CDerive::deriveBranch(const CEvaluationNode* node, const CCopasiObject * pObject,
std::vector<const CEvaluationNode*>& env,
//std::vector<const CCopasiObject*>& objenv,
const CEvaluationTree* pTree,
bool simplify)
{
CEvaluationNode * newNode = NULL;
const CEvaluationNodeOperator * pENO = dynamic_cast<const CEvaluationNodeOperator*>(node);
if (pENO)
{
if (!pENO->getLeft() || !pENO->getRight()) return NULL;
CEvaluationNode * pLeftDeriv = deriveBranch(pENO->getLeft(), pObject, env, pTree, simplify);
if (!pLeftDeriv) return NULL;
CEvaluationNode * pRightDeriv = deriveBranch(pENO->getRight(), pObject, env, pTree, simplify);
if (!pRightDeriv) {delete pLeftDeriv; return NULL;}
// we now know that derivations of the left and right branch exist
switch ((CEvaluationNodeOperator::SubType) CEvaluationNode::subType(pENO->getType()))
{
case CEvaluationNodeOperator::MULTIPLY:
{
CEvaluationNode * pLeftCopy = copyBranch_var2obj(pENO->getLeft(), env);
CEvaluationNode * pRightCopy = copyBranch_var2obj(pENO->getRight(), env);
CEvaluationNode * tmpNode1 = multiply(pRightCopy, pLeftDeriv, simplify);
CEvaluationNode * tmpNode2 = multiply(pRightDeriv, pLeftCopy, simplify);
return add(tmpNode1, tmpNode2, simplify);
}
break;
case CEvaluationNodeOperator::DIVIDE:
{
CEvaluationNode * pLeftCopy = copyBranch_var2obj(pENO->getLeft(), env);
CEvaluationNode * pRightCopy = copyBranch_var2obj(pENO->getRight(), env);
//numerator
CEvaluationNode * tmpNode1 = multiply(pRightCopy, pLeftDeriv, simplify);
CEvaluationNode * tmpNode2 = multiply(pRightDeriv, pLeftCopy, simplify);
CEvaluationNode * minusNode = subtract(tmpNode1, tmpNode2, simplify);
minusNode->compile(NULL);
//denominator
CEvaluationNode * powerNode = power(copyBranch_var2obj(pENO->getRight(), env),
new CEvaluationNodeNumber(CEvaluationNodeNumber::INTEGER, "2"),
simplify);
return divide(minusNode, powerNode, simplify);
}
break;
case CEvaluationNodeOperator::PLUS:
return add(pLeftDeriv, pRightDeriv, simplify);
break;
case CEvaluationNodeOperator::MINUS:
return subtract(pLeftDeriv, pRightDeriv, simplify);
break;
case CEvaluationNodeOperator::POWER:
{
// b-1
CEvaluationNode * tmpNode = subtract(copyBranch_var2obj(pENO->getRight(), env),
new CEvaluationNodeNumber(CEvaluationNodeNumber::INTEGER, "1"),
simplify);
// a^(b-1)
CEvaluationNode * powerNode = power(copyBranch_var2obj(pENO->getLeft(), env), tmpNode, simplify);
// b*a'
tmpNode = multiply(copyBranch_var2obj(pENO->getRight(), env),
pLeftDeriv, simplify);
// ln a
CEvaluationNodeFunction * funcNode = new CEvaluationNodeFunction(CEvaluationNodeFunction::LOG, "ln");
funcNode->addChild(copyBranch_var2obj(pENO->getLeft(), env)); // add a
// a * b' * ln a
CEvaluationNode * tmpNode2 = multiply(copyBranch_var2obj(pENO->getLeft(), env),
multiply(pRightDeriv, funcNode, simplify),
simplify);
// b*a + a*b * ln a
CEvaluationNode * plusNode = add(tmpNode, tmpNode2, simplify);
// a^(b-1)*(b*a + a*b * ln a)
return multiply(powerNode, plusNode, simplify);
}
break;
default:
break;
}
}
const CEvaluationNodeVariable * pENV = dynamic_cast<const CEvaluationNodeVariable*>(node);
if (pENV)
{
if (!env[pENV->getIndex()])
return NULL;
//basically just expand the tree.
return deriveBranch(env[pENV->getIndex()], pObject, env, pTree, simplify);
}
const CEvaluationNodeNumber * pENN = dynamic_cast<const CEvaluationNodeNumber*>(node);
if (pENN)
{
newNode = new CEvaluationNodeNumber(CEvaluationNodeNumber::INTEGER, "0");
return newNode;
}
const CEvaluationNodeObject *pENObj = dynamic_cast<const CEvaluationNodeObject*>(node);
if (pENObj)
{
//first check whether the object is the derivation variable
if (pObject->getCN() == pENObj->getObjectCN())
{
//std::cout << "*";
return new CEvaluationNodeNumber(CEvaluationNodeNumber::INTEGER, "1");
}
//now we need to check if we know something about the object so that it needs to be expanded
const CCopasiObject * tmpObj = (const CCopasiObject *)pENObj->getObjectInterfacePtr();
if (!tmpObj)
return NULL;
//object is a concentration?
if (tmpObj->getObjectName() == "Concentration")
{
//std::cout << "Concentration found" << std::endl;
//In this context, the concentration is expanded as "amount of substance/volume"
std::string tmpstr = tmpObj->getObjectParent() ? "<" + tmpObj->getObjectParent()->getCN() + ",Reference=ParticleNumber>" : "<>";
CEvaluationNodeObject* amount = new CEvaluationNodeObject(CEvaluationNodeObject::CN, tmpstr);
amount->compile(pTree);
tmpstr = tmpObj->getObjectAncestor("Compartment") ? "<" + tmpObj->getObjectAncestor("Compartment")->getCN() + ",Reference=Volume>" : "<>";
CEvaluationNodeObject* volume = new CEvaluationNodeObject(CEvaluationNodeObject::CN, tmpstr);
volume->compile(pTree);
CEvaluationNodeObject* volume2 = new CEvaluationNodeObject(CEvaluationNodeObject::CN, tmpstr); //we need this node twice
volume2->compile(pTree);
CEvaluationNode* damount = deriveBranch(amount, pObject, env, pTree, simplify);
CEvaluationNode* dvolume = deriveBranch(volume, pObject, env, pTree, simplify);
// A / V - A*V /V^2
return
subtract(divide(damount, volume, simplify),
divide(multiply(amount, dvolume, simplify),
power(volume2, new CEvaluationNodeNumber(CEvaluationNodeNumber::INTEGER, "2"), simplify),
simplify),
simplify);
}
//TODO:
//object is an object with an assignment
//object is dependent species
//object is a reaction rate
// otherwise return 0.
return new CEvaluationNodeNumber(CEvaluationNodeNumber::INTEGER, "0");
}
const CEvaluationNodeCall *pENCall = dynamic_cast<const CEvaluationNodeCall*>(node);
if (pENCall)
{
//is it a function?
const CFunction * tmpFunction = dynamic_cast<const CFunction*>(pENCall->getCalledTree());
// const std::vector<CEvaluationNode *> getListOfChildNodes() const {return mCallNodes;}
//create call environment for the called function
std::vector<const CEvaluationNode*> subenv;
size_t i, imax = pENCall->getListOfChildNodes().size();
subenv.resize(imax);
for (i = 0; i < imax; ++i)
{
CEvaluationNode* tmpnode = copyBranch_var2obj(pENCall->getListOfChildNodes()[i], env);
compileTree(tmpnode, pTree);
subenv[i] = tmpnode;
}
return deriveBranch(pENCall->getCalledTree()->getRoot(), pObject,
subenv,
pTree, simplify);
}
return newNode;
}